EGID Express

EPC2 transcriptional response to eosinophils and IL-13 (2021)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Dunn et al, 2021
https://doi.org/10.1038/s41385-021-00400-y

Experimental Design:

RNA sequencing was performed to quantify transcripts present in EPC2 cells untreated, co-cultured with human eosinophils, co-cultured with human eosinophils and treated with IL-13, and treated with IL-13.

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Eosinophil transcriptional response to IL-5, EPC2 coculture, and EPC2 colcuture with IL-13 (2021)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Dunn et al, 2021
https://doi.org/10.1038/s41385-021-00400-y

Experimental Design:

RNA sequencing was performed to quantify transcripts present in human eosinophil cells untreated, treated with IL-5, co-cultured with EPC2 cells, and co-cultured with EPC2 cells and treated with IL-13.

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Eosinophil and EPC2 transcriptional response to soluble mediators (2021)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Dunn et al, 2021
https://doi.org/10.1038/s41385-021-00400-y

Experimental Design:

Multiplex analysis was performed to quantify transcripts present in human eosinophil and EPC2 cells supernatants. Cells were treated with either IL-5 or IL-13 and either in mono-culture or co-culture.

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EoE Transcriptome by RNA Sequencing (2014)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Sherrill et al, 2014
https://doi.org/10.1038/gene.2014.27

Experimental Design:

RNA sequencing was performed to quantify transcripts present in esophageal biopsy specimens obtained from 6 healthy controls (Control) and 10 patients with active EoE (EoE).

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Kinetics of esophageal epithelial cell line (TE-7) transcriptional response to IL-13 (2014)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Rochman et al, 2014
https://doi.org/10.1038/mi.2014.109

Experimental Design:

TE-7 cells (a human esophageal epithelial cell line) were stimulated with IL-13 (100 ng/ml) for 2h, 6h, or 24h. Transcript levels were quantified by RNA sequencing. Untreated cells (Control_2h, Control_4h, Control_24h); IL-13-treated cells (IL-13_2h, IL-13_6h, IL-13_24h).

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Gene expression of undifferentiated EPC2 (monolayer), differentiated EPC2 (ALI), and differentiated SPINK7-silenced EPC2 (ALI) (2018)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Azouz et al, 2018
https://doi.org/10.1126/scitranslmed.aap9736

Experimental Design:

A telomerase-immortalized human esophageal epithelial cell line (EPC2 cells) was transfected with either non-silencing control shRNA or SPINK7 shRNA. Cells were grown either in monolayer culture (undifferentiated) or in air liquid interface (ALI) cultures (differentiated). Transcript levels of the following types of cells were determined: cells transfected with non-silencing control shRNA and grown in monolayer culture (Undif_NSC); cells transfected with non-silencing control shRNA grown at the ALI (NSC); cells transfected with SPINK7 shRNA grown at the ALI (SPINK7_silenced).

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Gene expression of undifferentiated EPC2 (monolayer), differentiated EPC2 (ALI), and differentiated EPC2 (ALI) +/- IL-13 (2014)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Sherrill et al, 2014
https://doi.org/10.1038/mi.2013.90

Experimental Design:

A telomerase-immortalized human esophageal epithelial cell line (EPC2 cells) was grown submerged in monolayer culture (undifferentiated) for 8 days, or were grown submerged in monolayer culture for 8 days followed by 6 days of culture at the air liquid interface (differentiated). In some cases, cells were treated with IL-13 (100 ng/ml) during the 6 days of ALI culture. Transcript levels of the following conditions were assessed by RNA sequencing: Day_0: cells grown submerged for 8 days; Day_6: cells grown submerged for 8 days and then grown at the ALI for 6 additional days; Day_6_IL-13: cells grown submerged for 8 days and then grown at the ALI for 6 additional days in the presence of IL-13.

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Esophageal Gene Expression (2006)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Blanchard et al, 2006
https://doi.org/10.1172/JCI26679
Blanchard et al, 2007
https://doi.org/10.1016/j.jaci.2007.10.024
Caldwell et al, 2010
https://doi.org/10.1016/j.jaci.2010.01.038

Experimental Design:

RNA isolated from distal esophageal tissue was subjected to genome-wide transcript profile microarray analysis. Experimental groups: NL: control; CE: chronic esophagitis; EoE: active EoE; EoE+FP+R: fluticasone responder; EoE+FP+NR: fluticasone non-responder.

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Gastric Gene Expression (2007)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Blanchard et al, 2007
https://doi.org/10.1016/j.jaci.2014.07.026

Experimental Design:

RNA isolated from gastric antrum tissue was subjected to genome-wide transcript analysis by microarray analysis. Experimental groups: control and active eosinophilic gastritis (EoG).

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Transcriptional response of primary esophageal epithelial cells to IL-13 (2014)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Caldwell et al, 2014
https://doi.org/10.1016/j.jaci.2007.10.024

Experimental Design:

Human primary esophageal epithelial cells from patients with EoE were cultured in the presence or absence of IL-13 (100 ng/ml) for 48 h, and the mRNA was subjected to genome-wide transcript profile microarray analysis. The data from the IL-13-stimulated cells were normalized pairwise to unstimulated controls.

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EoE Diagnostic Panel: EoE Endotypes (2018)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Primary publication:
Shoda et al, 2018
https://doi.org/10.1016/S2468-1253(18)30096-7

Experimental Design:

RNA was isolated from distal esophageal tissue of 86 individuals with active EoE. The RNA was subjected to EDP analysis, which quantifies 96 individual gene transcripts. Graphs depict the -deltaCt value -(ct of GAPDH – ct of gene of interest) for each individual. Experimental groups: EoEe1: EoE endotype 1; EoEe2: EoE endotype 2; EoEe3: EoE endotype 3.

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Single cell RNA sequencing of T-cells (2019)

Gene:

Type of graph:

Violin Plot

Ridge Plot

Separate by EoE/Remission/Normal

Primary publication:
Wen et al, 2019
https://doi.org/10.1172/JCI125917

Experimental Design:

Single-cell transcriptome profililng of esophagus biopsies from patients with active eosinophilic esophagitis (EoE, n=11), in remission (n=6), and without disease (n=5).

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Gene expression profiling of bone marrow and esophagus from PIR-B KO mice by microarray (2016)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Primary publication:
Ben Baruch-Morgenstern et al, 2016
https://doi.org/10.4049/jimmunol.1501873

Experimental Design:

17 samples were analyzed in this experiment. The experiment was designed with 3 replicates for each treatment/genotype/tissue (Dox and no Dox/wildtype and knockout/bone marrow and esophagus), with the exception of the sample wildtype bone marrow no Dox where 1 replicate was dropped due to low hybridization signal. The no Dox and wildtype samples are controls for the treatment and background of the mice. Experimental groups: bm_WT_noDox: bone marrow, wildtype, no Dox; bm_KO_noDox: bone marrow, PirB knockout, no Dox; bm_WT_Dox: bone marrow, wildtype, Dox; bm_KO_Dox: bone marrow, PirB knockout, Dox; eso_WT_Dox: esophagus, wildtype, Dox; eso_KO_Dox: esophagus, PirB knockout, Dox.

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EoC RNASeq (2022)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Shoda et al., 2022
https://doi.org/10.1053/j.gastro.2022.01.022

Experimental Design:

RNA sequencing was performed to quantify transcripts present in colon biopsy specimens obtained from 8 control individuals (Non_EoC) and 6 patients with active EoC (Active_EoC).

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EoG Transcriptome by RNA Sequencing (2020)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Primary publication:
Shoda et al, 2020
https://doi.org/10.1016/j.jaci.2019.11.007

Experimental Design:

RNA sequencing was performed to quantify transcripts present in gastric biopsy specimens obtained from 12 healthy controls (Non-EoG) and 9 patients with EG (EoG).

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Mouse Eosinophils +/- IL4 or IL33 (2013)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Primary publication:
Bouffi et al, 2013
https://doi.org/10.4049/jimmunol.1301465

Experimental Design:

RNA sequencing was performed to quantify transcripts present in LDBM Mouse Eosinophils untreated, treated with IL-4, or treated with IL-33 at 1 hour and 4 hours.

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Effect of PPIs omeprazole and esomeprazole on gene expression in EPC2 cells (2020)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Rochman et al, 2020
https://doi.org/10.1016/j.jaci.2020.09.039

Experimental Design:

For the monolayer cultures, EPC2 cells were seeded at a density of 2.5x10^5 cells/well in KSFM in a 24-well plate. The next day, the medium was replenished. After 24 hours, stimulants were added in a total of 350 to 500mL of fresh medium for 24 hours. IL-13 was added to a final concentration of 100 ng/mL unless otherwise indicated. Omeprazole and esomeprazole were dissolved in DMSO to the stock concentration of 100 mM, aliquoted into 10-mL amounts, and stored at –80°C. PPIs were thawed once and used at a working concentration of 100mM; cells were pretreated with the PPIs for 1 hour before adding IL-13 to the medium. GNF-351 was dissolved in DMSO to a 20 mM stock concentration. The stock was aliquoted in 10-mL doses and stored at –80°C. Cells were pretreated with GNF-351 at a final concentration of 2mM for 30 minutes before adding PPIs.

RNA sequencing was performed with high-quality RNA (RNA integrity number > 8) by using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria, catalog no 015.96).

Libraries were diluted to final concentrations of 5 nM and sequenced on a HiSeq 4000 Illumina sequencing machine at the Genomics and Cell Characterization Core Facility at the University of Oregon with 100- to 150-bp-length single reads.

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EPC2 +/- PPI Multiplex (2020)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Rochman et al, 2020
https://doi.org/10.1016/j.jaci.2020.09.039

Experimental Design:

Multiplex analysis was performed by Eve Technologies (Calgary, Canada) using the Human Cytokine Array/Chemokine Array 65-Plex Panel (HD65).

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Effect of IL-13 and Vitamin D on gene expression in EPC2 cells (2022)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Brusilovsky et al, 2022
https://doi.org/10.1136/gutjnl-2022-327276

Experimental Design:

The contribution of vitamin D (VD) deficiency to the pathogenesis of allergic diseases remains elusive. We aimed to define the impact of VD on esophageal allergic inflammation. To this end, we examined the potential clinical relevance of the esophageal epithelial cell (EPC2) transcriptional responses to IL- 13 or VD. Cells were grown in the monolayer culture at a super-confluent state (1×106 cells/cm2). Cells were treated with recombinant human IL- 13 (100 ng/ mL) and/or VD (1,25- dihydroxycholecalciferol; 100 nM) and subjected to bulk RNA sequencing.

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Mouse IL13Tg Esophagus (2010)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Primary publication:
Zuo et al. 2010, JI
https://www.jimmunol.org/content/185/1/660

Experimental Design:

Bi-transgenic mice (CC10-iIL-13) were generated in which IL-13 was expressed in a lung-specific manner that allowed for external regulation of the transgene expression, as previously described(13).

RNA from the esophagus or lung of IL-13 inducible transgenic mice obtained after 30 days of DOX or NO-DOX treatment was subjected to gene chip analysis using MOE 430 2.0 chips as previously reported (15). Gene transcript levels were determined using algorithms in the Microarray Analysis Suite and GeneSpring software (Silicon Genetics). For comparison with human EoE, genes were translated to human homologues represented on the human U133 chip using GeneSpring software and compared to microarray results previously described(8, 15). Welch T test and fold change cut-off were performed. The correlation between IL-13 expression and numbers of dysregulated genes were also analyzed using GeneSpring software.

2 NO-DOX samples and 3 DOX samples

MOE 430 2.0 chips - Affymetrix
Composition of probe sets can be identified/analyzed on NetAffx
https://www.affymetrix.com/site/login/login.affx?toURL=/analysis/netaffx/index.affx

References:
8 - https://pubmed.ncbi.nlm.nih.gov/18073124/
13 - https://pubmed.ncbi.nlm.nih.gov/14757645/
15 - https://pubmed.ncbi.nlm.nih.gov/16453027/

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EoD RNAseq (2022)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Dot plot: individual samples

Experimental Design:

RNA sequencing was performed to quantify transcripts present in duodenal biopsy specimens obtained from non-EoD controls (NL), patients with duodenal eosinophilia (DE), or patients with eosinophilic duodenitis (EoD). Graphs were depicted by the TPM for each individual.

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Single Cell Whole Biopsy RNAseq (2022)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Primary publication:
Ben-Baruch Morgenstern et al. 2022, JACI
https://doi.org/10.1016/j.jaci.2022.02.025

Rochman et al. 2022, JCI
https://doi.org/10.1172/jci.insight.159093

Experimental Design:

Esophageal biopsies were obtained from patients with active EoE (n = 5), patients with EoE in histologic remission (n = 3), and control individuals with histologically normal esophageal biopsies and no history of esophageal disease (n = 2) and were subjected to 10X scRNA-sequencing.

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Mast Cell Only Single Cell RNAseq (2022)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Primary publication:
Ben-Baruch Morgenstern et al. 2022, JACI
https://doi.org/10.1016/j.jaci.2022.02.025

Experimental Design:

Graph

Esophageal Epithelium in Allergic Inflammation (2022)

Gene:

Type of graph:

Feature Plot

Violin Plot

Ridge Plot

Primary publication:
Rochman et al. 2022, JCI
https://doi.org/10.1172/jci.insight.159093

Experimental Design:

Graph

Esophageal Spheroids from EPC2 (2024)

Gene:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Rochman et al. 2024, Am. J. Physiol. Gastrointest. Liver Physiol
https://doi.org/10.1152/ajpgi.00197.2024

Experimental Design:

We aimed to characterize esophageal epithelial differentiation in vitro in a three-dimensional (3-D)-organoid culture system derived from EPC2 cells. This approach was previously used to mimic esophageal epithelial differentiation and changes associated with esophageal diseases in humans and mice. IL-13 was added at 20 ng/ml from Day 3 until Day 11.

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EoE Proteomic Signature

Protein:

Type of graph:

Bar graph: group average +/- SEM

Box and whisker plot

Bar graph: individual samples

Primary publication:
Rochman et al. 2023, JCI
https://doi.org/10.1172/jci.insight.172143

Experimental Design:

31 esophageal biopsies were collected from EoE and control patients. Biopsies were sonicated for 4 minutes in 110 μL of 8 M urea with protease inhibitors. Samples were spun down at 12,000g for 10 minutes, and the supernatant was collected for analysis. The bicinchoninic acid (BCA) protein assay was used to determine the protein concentration of each sample. Following protein digestion, samples were subjected to LC-MS/MS experiments. Peptides were trapped on an Acclaim C18 PepMap 100 trap column (5-μm particles, 100-Å pores, 300-μm i.d. × 5 mm, Thermo Fisher Scientific) and separated on a PepMap RSLC C18 column (2-μm particles, 100-Å pores, 75-μm i.d. × 50 cm, Thermo Fisher Scientific) at 40°C. The RAW MS files were processed with MaxQuant (version 2.0.3.0, Max Planck Institute, Munich, Germany) and searched with the Andromeda search engine against a human UniProt FASTA database.

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Gene/Protein:

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EPC2 transcriptional response to eosinophils and IL-13 (2021)

P-value

Eosinophil transcriptional response to IL-5, EPC2 coculture, and EPC2 colcuture with IL-13 (2021)

p-value

Eosinophil and EPC2 transcriptional response to soluble mediators (2021)

p-value

EoE Transcriptome by RNA Sequencing (2014)

p-value

Kinetics of esophageal epithelial cell line (TE-7) transcriptional response to IL-13 (2014)

Gene expression of undifferentiated EPC2 (monolayer), differentiated EPC2 (ALI), and differentiated SPINK7-silenced EPC2 (ALI) (2018)

p-value

Gene expression of undifferentiated EPC2 (monolayer), differentiated EPC2 (ALI), and differentiated EPC2 (ALI) +/- IL-13 (2014)

p-value

Esophageal Gene Expression (2006)

p-value

Gastric Gene Expression (2007)

p-value

Transcriptional response of primary esophageal epithelial cells to IL-13 (2014)

p-value

EoE Diagnostic Panel: EoE Endotypes (2018)

p-value

Single cell RNA sequencing of T-cells (2019)

Gene expression profiling of bone marrow and esophagus from PIR-B KO mice by microarray (2016)

p-value

EoC RNASeq (2022)

p-value

EoG Transcriptome by RNA Sequencing (2020)

p-value

Mouse Eosinophils +/- IL4 or IL33 (2013)

Effect of PPIs omeprazole and esomeprazole on gene expression in EPC2 cells (2020)

p-value

EPC2 +/- PPI Multiplex (2020)

p-value

Effect of IL-13 and Vitamin D on gene expression in EPC2 cells (2022)

p-value

Mouse IL13Tg Esophagus (2010)

p-value

EoD RNAseq (2022)

p-value

Single Cell Whole Biopsy RNAseq (2022)

Mast Cell Only Single Cell RNAseq (2022)

Esophageal Epithelium in Allergic Inflammation (2022)

Esophageal Spheroids from EPC2 (2024)

p-value

EoE Proteomic Signature

p-value

Search All Experiments (single-cell RNAseq experiments excluded)

Abbreviation Glossary